My New Eyes
by The Smiling Shadow
Summary: The War is over. Deep within the walls of Machine City Neo lives again. But he is confined to the artificial walls, never to go back to Zion. But change is about to happen, change that the machines cannot deny him. It begins with Smith's rebirth.
1. A New Home

The war is over.

A city is in ruins, and yet there is celebration away from the metal walls, deep into the earth in the caves, does what remains of Zion sing. Lovers of war are united, or forever separated. Some have together died. The city that lies in ruins, centuries of building, crumbled in a matter of minutes. In this city, do the bodies of man and machine lay. Together and intertwined, they seem somehow connected. A machine body lies above a human's, and somehow from a distance it appears as if the machine is protecting the human. But away from the smell of death and burning embers, is the celebration. The drumming of music, and the united cries "We are Free!"

The humans dance, and in unison scream to the heavens, to whatever God there may be, to the sky that is no longer there, to the stars they can no longer see. People hold each other. Some fall to their knees and cry in such a sight.

"Is this what it is to be free?"

This was the war that united all men, of any color, any race, any religion. This was the war where racism, sexism, and prejudice died. This was the war where man was just man, fighting for what all man should have, freedom! Believed what you want to believed, you are different from me, but you are still my brother! You still have bones that can break, and blood that can be spilled. This was the war where all was one!

This was the war, the final war, they all say.

And now in peace, they shall somehow find a way to make more brothers. Somehow they must look at a man made of metal, and say, your bones are steel, but they can break, your blood is oil, but it can be spilled, and you are my brother. Somehow their enemies must unite with them, they shall find a way to be truly united with all beings.

It is what he would have wanted.

This is the war that made unison. This is the war that forces unison. This is the war that depended on him!

A man named Morpheus holds out his arms to the people of Zion, with a woman named Niobi by his side.

"This is for him! Let us scream to him! Let us show him, we know, we know. Neo! The One! Thank you for this moment!"

Believers, and nonbelievers unite, and they scream to him, wherever he may be. Weather he was a Messiah or not, does not matter, he was the one that ended this war.

Sentinels, Machine guardians, Machine murders now stand at the edge where metal meets with Earth. They stand on the metal, as if afraid of this earth, that was not made by man's hands or their own. With red eyes they blink and watch these humans that they were only going to kill moments ago, celebrate in freedom. It was only when the Matrix was first created did Machines ever celebrate like this. What was the beginning of this war but a fight for Machine rights? In the beginning Machine wanted freedom, Machine wanted the right to live, Machines wanted the right to say they too had a soul. Should they now celebrate again?

The humans look across to these Sentinels, still standing at the edge where the world ends. And it is Kid who steps forth, and motions for them to come.

"Come on, it's okay…" He says to them.

How long has it been, since a machine has ever listened to a human speak to them in peace? Since when was it did a Machine not hear a scream or weep from man?

And this is the first time Machine has stepped into the caves of Zion.

The celebration will continue for days and days. Morals will be lost, and in the mass of emotion, love making will occur on the grounds, blood will be shed for primal rituals, tears will be collecting, and the screaming will never stop. Forget their turmoil, forget the difficulties and negotiations that will occur in the upcoming days. This is now, this is their first moments of freedom.

Here they are born again.

All because of him.

Soon authorities will take over, planning will begin. Bodies will be buried, Machines will carry their dead back to their home, where they will either be repaired, or buried in their own Machine way. Debris shall be cleared, ships repaired, homes rebuilt, and Machine will show Man how to make the soil fertile again. And within a year, the first tree in Zion will grow. Plans on the city of Babylon will begin, somewhere closer to the surface, and theories on how to clear the sky will clear.

Machines will fly in Zion space, and for the first time in over five hundred years will a Machine speak in a human tongue, of not ones or zeros, radio signals, but words. For the first time in over five hundred years will Machines be made and upgraded in the distant image of humans, in order to show their willingness for this peace to work. Machines with humanoid bodies, long and skinny, but strong and sturdy. Machines with two legs, and two arms, but the face of Sentinels to show, they are still machines. These humanoids will walk among the Zionists, they will speak in their tongue, and they will shake their hands.

It will be these humanoids, these androids, that will be the ambassadors.

For the first time in five hundreds of years will man's foot step in Machine city. Councilors will meet with Machine, and they will discuss for hours negotiations. There will be many resolutions, some confrontations, and many misinterpretations as well as curios questions.

But there is still one question that rings within the human collective.

Where is his body?

The Machines remain in silence.

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"I carry your heart with me, I carry it in my heart. I am never without it, anywhere I go you go, my dear; and whatever is done by only me is your doing, my darling. Here is the deepest secret nobody knows, here is the root of the root and the bud of the bud and the sky of the sky of a tree called life; which grows higher than the soul can hope or mind can hide. And this is the wonder that's keeping the stars apart, I carry your heart, I carry it in my heart."

He puts down the flower by her grave, and a question is asked.

"Hm? Oh nothing, it's just a poem I had to memorize in high school. It always makes me think of her." He says.

He smiles at her grave, and for the first time in weeks, tears begin to crawl down his face from restored black eyes.

"I'm all right…I'm all right."

He didn't even know the oceans still existed. But here he was, standing only feet from the beach. He looked out upon it, the now green water washing up to the shores, and crashing into the metal cliffs where bone and steel are fused. There was a certain disturbing beauty in it, he could not describe. He was never one for a day at the beach, the water was cold, and the sand stung whenever the other boys kicked it into his face.

It was dark then, as it was always dark there with sky having died.

An area has been cleared on one of these metal cliffs, soil has been made fertile again, and now flowers grow around her, and he likes to think they only grow because she is there. There is a gravestone of clean metal, and on it are the words, "My Trinity, My Reason, My Purpose. The War would never have ended without you." He smiles at it, standing above her in the middle of the flowers.

His name is Neo. He is not dead.

He looks over at the crouched Sentinel, doing its own respective bow. He taps his hand over it, like a pet, and then it looks up at him with red eyes.

"Come on, Edison, let's go. They said only two hours this time." Neo says.

He jumps onto the Sentinel's back, and it begins to gently lift from the ground, flying feet above the debris, looking for a set path that has been made for him. He has named this Sentinel. It seemed a human enough thing to explain to the machines at first, the act of naming something, making it seem personal. Edison was personal, Edison was made as his, to be his guardian, protector, and equal keeper. Neo just thought naming it Edison was cute.

"How long has it been Edison?" Neo asks as they float away.

Edison speaks without words, and Neo nods.

"That long?"

Edison replies.

"Oh, yes, I slept most of it didn't I? Still…six months…that's how long I got to stay with her. It should be around a year now…I was freed, and I met her."

Neo smiles, then leans forward, looking upside down on Edison while still sitting on his back.

"That means you're six months old, Edison, congratulations!"

The Sentinel makes a reaction that a human could never understand. The little arms on its front move up in a cheer, and its eyes blink with what could be joy. Edison, Neo's Sentinel, says thank you. Neo smiles and rises, sitting back on the Sentinel's back. Edison finally stops and lands onto the ground, with Neo jumping down, walking on a little path along the mountains of metal and bone.

Neo is the One. He is not dead.

Six months ago the war ended because of him. Six months ago was his body dragged and carried to the deepest depths of the machine city where no human had ever gone, no human that was never freed at least. Human technology even then has not advanced so far, as to bring the dead back to life. But Machine had. There was a limit of twenty four hours, this was the extent of how long one could be dead and brought back, by then the brain would be too deprived of oxygen, the entire body would be in the beginnings of decay. But Neo was only dead for what could be an hour at most. They are unsure how but Neo…

The One was always artificially made by them, but this One…this One was different. This One had grown beyond set perimeters. This One grew into something more, as did his counterpart, the Smith program.

The One no longer was the One, but something far greater. Their Source.

The procedure was a rather long one, having found that the human organs were already starting to deteriorate within him. The human body already betraying the mind that wants to live on. Blood had to be drained, metal was crafted to flesh. The spine was given steel, the stomach given plastic, and the now damaged eyes were plucked out. This was already difficult, given the fact the machine had to work around their own work, the plugs given to this One at birth. Some had to be removed, and others had to be replaced. Little hands, micrometers long worked all over the body that was Neo, hands more delicate than man's. Hands that could create, save, and destroy like mans'. And for an hour or so into the procedure, Neo was lying on a cold medical table, his chest folded open. The machines were immune to such sights, but somehow even they were disturbed. The back of The One's skull is now metal, the plug on the back of his neck that connected to the brainstem is larger, compensating really.

Anyway, at the end of it all, the rebuilding and restoring, they pumped air into his lungs, and gave the blood back to the veins. The heart was made to beat, and electric pulses were sent through the brain to wake the mind again. In all technicality Neo was alive again.

Then the chest was sewed back together, the head stapled, and drugs to numb the mind from the pain.

And then Neo opened his eyes again.

The machines had given new eyes, though were not able to save his old ones, burnt out of existence, like they had exploded inside his skull. Eyelids were nearly fused together, covering nothing but empty holes in the skull. Machines took away the dead flesh, and replaced it, they crafted eyelids, complete with eyelashes and eyebrows. Then they filled the empty holes with black lenses. Eyes now black, no pupils, but all black, much like the machines'. They aren't his anymore, and he misses that. He sort of liked his Asian Almond eyes, no one ever believed him when he said his dad was Asian, that's where his brown slanted eyes came from. He sighed at the beginning, seeing his lost of sight, as the loss of another thing that identified him as human. They see just the same, designed with no enhancements that his still human bound brain could not handle. They see like his old eyes, but they are not.

His new eyes.

Neo did not regain consciousness for an estimated eight hours, but when he did it took him a moment to realize where he was. His head began to shake with life, and he opened his new eyes, still visible through his nearly transparent and young eyelids. He saw the light above him, and cold machine hands cupped his face.

"Is this Heaven?" He asked and coughed. "I'm atheist, I'm sorry…is this Heaven?"

Neo proceeded to cough up some blood, and little stomach acid, which would have hurt his throat if not for the fact the machines had replaced it with a metal tube.

"Neo…" said the collective Machine mind as softly as it could.

"Trin?"

"No, Neo…"

Neo would then focus and see it was a machine holding him up. He would kick it away, and crawl off his bed, falling and rising, backing into a living machine wall. He would scream and thrash, and kick, and punch as the machines neared him and held him. The machines would then back away and lower what was their heads. And Neo would fall to the floor, tear ducts working again, and he would cry.

He broke some of the stitches on his chest, so the Machines guided him to a table, and one more human looking machine began to replace them. Neo stared at the machine, and the many others surrounding him.

"Why?" Neo asked.

"Clarify, please." Said the human looking machine in a rather fragmented voice.

"Why have you brought me back?" Neo said, angered.

"Because we had to, Neo." Said the Machine. "You, either intentionally or unintentionally have taken our living source, The Source, and if you had truly stayed dead the Source would have died with you, all machine would have died with you."

"That's what I did huh?"

The Machine nodded.

"Did you see it?" Neo asked. "Me and Smith?"

The Machine nodded.

"All Machine saw it."

"What happened?"

"Smith copied your shell in the Matrix, and he was believed to have won. But then your body here surged with pulses, your body being connected to the city, and all machines, took from the Source, and your body acted as a sort of bridge from us to Smith. You took the Source via your body, and put it in the Matrix, inside Smith. The Source, being the giver and taker of Machine life, took Smith's, seeing him as a Viral disease, and began deleting him from the inside out."

Neo slowly nodded.

"At least that is what we believe we observed." Finished the machine.

"Yeah…that sounds good to me."

Neo in all truth didn't really know what happened. He only knew that for a time he saw Smith, but then the images faded, and wherever he was, drifting in the dark, there was pain. Enormous unknown pain, trying to bind and control, trying to stop and cage. Then Neo tore light into the dark, and the tore began to grow, and the light consumed all, even him.

"What now?" Asked Neo. "What will you do with me? Can I go home?"

"No."

"Why not!" Yelled Neo.

"Because you'll die there. That is what man does, Neo." Said the machine. "They kill, and destroy. Especially the things that they say they love. Like yourself."

"They will not hurt me!"

"Another characteristic that defines a human is the lack of ability or refusal to learn from the past. They call you a Messiah, and what did they do to their last Messiah Neo? Humans grow envy, and from envy comes resentment, and resentment brings anger and destruction. It only takes one corrupt human being to destroy and taint everyone else. Someone, somewhere in that city hates you Neo, and even as you saved them, still hates you, and if you go back they will find a way to kill you, kill us." Said the machine calmly. "We will not allow you as our creation and creator to be destroyed again."

Neo stared at them all, and the machine finished the last of the stitches. Neo made fists.

"I want to go home!" He yelled.

"This is your home." Said the Machines.

"No!"

And Neo punched the Machine that stood in front of him, and the Machine's face imploded, and it fell down dead. Neo held out his fist in amazement, his hand felt fine, even as a knuckle began to bleed. He was stronger now…

"I want to go home!" He yelled at the living walls. "All my life you've told me you controlled me! Not this time! NOT THIS TIME! I WANT TO GO HOME!"

And Neo, no longer the One, but the Source, the giver and taker of machine life, took theirs. The surrounding Machines fell down dead in a burst of electricity, or implosion of CPU cavities. In the One's anger he had killed them all.

And this was how it was for the next few weeks. Neo was left alone in seclusion under the supervision of machines. He left the hospital and entered the many corridors and hallways that made up Machine City. He was allowed to look, to touch, and think alone.

Neo alone, tried to come to the conclusion and realization that this would be his home, because he knew the Machine's words were true. It was a better story ending besides, if he gave his life for them. He imagined himself in the history books of the Zion elementary school, they would find pictures of him as a kid wouldn't they? Of his fights and battles. People would study his moves, and his life. There would be mother's telling their sons the bedtime story of Neo.

Boy, he was a life to tell, he laughed at himself. Troubled boy searching for reason to live, an atheist at heart, a man who just doesn't give a flying fuck, becomes Jesus and saves the world from robots.

He laughed at it, the whole idea of it, it was ridiculous. But really…he'd be remembered, isn't that what people truly want in life? To be remembered, and to thus live forever? Anyone would give anything to be him, but he would give anything to be them. How many times did he sit and ask whoever was out there, why him? But in all truth there was no answer, it was a lottery between six billion souls who would be the One, and apparently he won, or lost.

He began to swallow the fact that he would spend all of eternity with Machines. And he went back to them, the Machines, Deux ex Machina and all. And he asked of them, what did they want from him.

Life they said, to find peace with mankind, they said.

Neo said okay.

It became a symbiotic relationship really, as it had between man and machine for all time. Neo provided life, and Machine provided protection. Just as the Matrix provided a life for Man, and life for Machines. Neo thought much about who he was, what he was, and just decided in an old Thomas Anderson sort of way, to fuck it. Forget about trying to think it out, it wasn't worth it. This was what was happening, he accepted it, he was the Messiah for man and machine, and there he was alive.

And he stood above the body of Trinity, dead for far too long to be brought back, too much internal damage, too beautiful to be cursed with living with him in this place. He wouldn't want her to come back to this, having her only reason to live is for his company. No, Trinity deserved more than that.

And if he could he would give her a life. All these things, all this power, and he couldn't do the one thing he wanted. He would have given her a life, hope. They'd have a home where trees grew and spring came with winter. A home with friends. A child. Secretly that's what Neo would have loved. Perhaps a girl, so he'd be hers. Daddy's little girl. He didn't have a name though…maybe Michelle like his mother… She'd have the whitest purest skin, with slanted blue eyes. Hair that had a curl like her mother, but a rather smooth face like his. Yes, he'd teacher her how to fly and everything.

But this was a life that he could never have. To be the One is to be alone, he supposed.

He said goodbye to her.

But the One was separated into two parts, and with one half alive, the second half was alive as well. Neo felt it before the Machines ever told him, it was in his chest, a puff of no air, like he was about to drown.

And here he is now. With his Sentinel named Edison, and his grave that he made for her. He walks the Desert of the Real, looking up at the ruins of a once great and greedy society. It is enough to make him cry, if he still had tear ducts. He jumps onto a random metal bone mountain and begins digging around, with Edison flying up towards him and helping.

Neo pulls out an Android's skull, and holds it up like Hamlet.

"Do you think he'll like this?" Neo asks.

Edison answers.

"I don't know what he wants, I didn't exactly get the chance to ask him." Neo says sitting down with the skull. "Can you give him a human body? He did that with Bane." Neo shakes his head. "I don't know…maybe he wants to feel with flesh…or maybe he doesn't even want to remotely look human."

Neo clutches the Android's skull.

"Maybe he'd want a body like you, Edison. But then…he'd probably try to kill me." Neo smiles. "Smith's crafty like that, the bastard."

Smith, the negative, the opposite, the antichrist.

With Neo's new found life, they also breathed life into him, and somewhere in the Matrix Smith began his life screaming. They were at first unsure of what to do with Smith. Unlike Neo he was weak, and broken. Whatever Neo did to him, it must have hurt. The program known as Smith was nearly corrupted, bits and pieces missing here and there, a burning hate still fueling the illusion of purpose. The program had reverted back to machines roots, meaning anger and hate no longer played a part even if they were still there. No, the program was searching for a subroutine on how to continue as it was, but such a subroutine was absent, gone in the destruction Neo caused. So the program ran a full system diagnostic and viral scan, though this tasks could not be completed. Errors erupted, and prevented any kind of progress.

The files that had data on speech and movement were corrupt, finally a solution came to ask for help. A connection was requested with the machine mainframe so that he may be repaired by them, but the connection kept being denied and failed.

And so the shadow of Smith had reach an end, corrupt and beyond self repair, the program was stuck in a never ending loop of trying to live again. Smith in all truth was no longer Smith, but just a broken program. Smith was it, not deserving a name. It sent out constant connection requests, as well as messages in ones and zeros at all frequencies for help. It sent out all remaining memory files, anything and everything. Images of a man named Neo, and two other men in suits. It sent recordings of screams and gun shots, a fragmented loop of the one word, "why?"

They isolated him in a machine construct, much like the Train station between reality and the Matrix. They showed Neo, and on a screen was the broken code of Smith. But Neo in all his powers saw him in that construct, lying on a non existent floor in nothing. The data that remained of the program struggled to maintain a visible shell, the image of itself often disappeared and reappeared, or was just deformed into green code.

"I want you to fix him, and give him a body." Neo said.

Neo had been studying up on a variety of Machine customs, their system. Programs could become Machines, Machines could become Programs. Neo knew it could be done. Yet the Machines screeched, speaking in words that no one but Neo could hear, they did not like the idea.

Neo stared at the skull and wondered who it once was. In all sense it looked human, only made of metal. He sighed, and wondered where this Android met his end. Was he brutally killed by man like Machines were, or did he loose whatever a Machine has of a life in battle?

"I think…I think Smith would want blood, but not have flesh. He'd want his face, and eyes, and voice, but not be human…" Neo looked up at Edison. "Can you do that?"

Edison spoke in silence for a length of time. Neo nodded. Then Edison asked why were they putting so much effort forth to repair the Smith program, when it was why Neo had died, why Neo's Trinity died.

And Neo laughed.

"The thing…" Neo began. "the weird thing about humans, is that no matter what they hate to be alone."

But you are not alone, says Edison.

"But Smith…Smith is different, Eddie. It's true whatever the hell he said…you know, he said we were equals, and opposites. And I felt it, and he denied it, that no matter how strong either of us got, we could never kill each other, not perminantly anyway…Smith and I, we have this connection, he's in me, and I am in him, even though he'd never admit it. But…I am the Messiah, he is the Antichrist, the negative to balance the positive. As long as I live he lives. So…we might as well spend eternity together…" Neo tried to explain.

Neo held up the skull of an android, and he looked at it, sighing. They were gathering body parts for Smith, metal components to fit into each other, a skull with an empty brain inside it, ready for Smith's to take it over. The Machines will fix Smith, and he will be given a body to spend with Neo in a reality he only entered for a time.

This was his life now, sometimes sick and withered with a body full of metal. Only able to stand the outside world from Machine City for two hours, and the farthest he can go is just a few miles, where there are only monuments of the war in the form of mountains of dead. A Messiah that shall withstand the test of time, and be in the shadows as the world around him changes. Fuck it, he thinks to himself, no more sad fucking thoughts, there's been enough of those.

Neo, with a new life, new body, and new eyes

He held the skull closely to him, knowing that it may soon be Smith's skull. He looked out into the distance knowing somewhere out there was Zion, his home. He wondered what was happening out there, what was happening without him. He could feel it from the ground he stood upon, the world was shifting, Zion was changing, and he was not there to witness it.

He would never be there again.

He frowned at this, and clutched the skull closely. This life…this fucking life… He should write a book or something…Neo, the One, the Source, taker and giver of life, with a power inside that remained dormant within the flesh and metal. Neo did not tell his Machine keepers or Machine children.

But holding Smith's future skull, Neo felt change in the air, like he had in the beginning of his birth has the One.

Something was about to happen, and he feared he would miss it. But somehow he knew he was wrong.

Soon the two hours ended as everything ends, Neo held with him a torso, arm, and skull that were intact for Smith. He got atop Edison, and they flew back to the Machine City.

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This may become a more of story, but for now all I have planned is a few chapters, though I've set it up in case I want to make it longer.

Will also be continuing Asylum very, very soon.

Anyway, next Chapter will bring the rebirth of Smith.

Next Chapter: Artificial Blue


	2. Artificial Blue

"God said onto Cain, 'Where is Abel, thy brother?' And Cain replied, 'I know not, am I my brother's keeper?"

Edison asked what Neo was saying.

"Nothing, just something that sounds appropriate…"

He was never a very religious man, Neo. But the seven-year-old Neo was in Catholic school upon his father's request. Although Neo barely remembers most of the teachings, there are some random Bible quotes that still remain in his head. He was known for causing trouble, with his nonstop questions, and ability to find loopholes in the text. When they were studying creationism, and the beginning of humanity, he had yelled out "EW! Cain married his sister!"

From fourth grade on Neo was enrolled in the public schools, but found no acceptance even in those places. He didn't understand why no one liked him, but with children someone must always be the outsider, the group just decided that was him.

The death of his mother, and the fall of his father into alcohol didn't help either.

Neo and Edison stood inside the hospital complex, where Neo's blood still stained the floor. A nice little window had been provided so that Neo could see the procedure taking place before him. The rebirth, recreation, recollection, revival of Smith, or however you wanted to call it. Body parts have been scavenged, new ones have been made, and many have been altered and upgraded.

And even new clothes have been made. Neo made it implicitly clear Smith would need a suit. The reasoning behind this escaped the Machines, but Neo told them he needed a suit. So they made one, if not crudely, but they made one, and creating cloth was not so simple anymore, but they were able to make some clothes for Neo, including a black trench coat. Just like good ol' times. The Machines did have a garden area, for they for destroying all life, did learn to appreciate the time when the world was alive. The garden was small and there was only one, with but a few plants. One tree, grass, roses, sunflowers, and cotton plants.

The body of Smith stood naked then, just a metal chassis with arms and legs, and no head. It hung limp from the wall as finished machines stood around it. All machines were unsure of what they were creating, but the Source, Neo with the power to take and give life wanted this, and they were rather more afraid of Neo than they were of Smith, who was at the time but a fragment of himself.

Smith's new head was in the hands of a rather smooth looking machine, as it was grafted what appeared to be skin over the face of the skull. Soon all the machines were grafting skin over the metal carcass as best they could. Though the skin looked transparent over the dark surface of black metal. It wasn't true skin, but an artificially made skin plastic. Upon Neo's request, they were giving Smith an image of what he was inside the Matrix. So scans were done of the image of Smith, and molds were created for his skin. The power cells were added, energy given by the Source to give life to the machine body. And soon red lights flickered on and off inside the chest of the body like the red eyes of a Sentinel. Clothing was the last to be put on, the poorly crafted suit was dressed on, and a tie to go with it all.

The headless body began taking its form.

Neo couldn't really get a good look at the new face and head of Smith, in the hands of the machine crafter. Skin was being held in place by bolts and straps. Artificial eyes like camera lenses were being connected, as the back of the skull was taken off to reveal the chips that made up all artificial minds. Hair was on thing the head lacked, otherwise it was a complete copy. No, the skull was given a face, but it ended at the forehead, and showed the machine being Smith was. Where skin ended, metal continued.

While this was happening, beside the hospital the machines were repairing what was left of Smith as it continued to send connection replies. The machines had back up files in storage of all programs ever created in all the Matrixes. And this back up file, though incomplete, was used to add what Smith was missing. Though memory could not be fully restored, subroutines were there. Walking patterns were given as well a blinking patterns to make it look random like humans. Speech was restored as well as a hundred different languages, some from cultures extinct. A history on human beings as well anatomy, and history of machines, along with blueprints. The history of the Matrix was given, and a variety of other things. In essence Smith was repaired.

But fearing Smith as the machines did, hundreds upon hundreds of fail safes to prevent a repeat of rebellion on Smith's part. Programs were different from solid machines, who possessed minds bound to programming. With programs there were no such boundaries, despite popular belief. The minds of programs and machines were different, and there was often a difficult transition between the two. But having Smith as a machine solid they were able to have more control over him.

The head was placed on, and somewhere inside Neo, he cringed.

And now, complete Smith was just sleeping. Plugs came from the wall into the skull, arms, and back. The program that was Smith sent a request for connection, and finally it was given an answer. Though it wasn't an answer completely, the reply demanded only one connection line, the program agreed. It was redirected through a single route, straight into the body that would be Smith's.

Neo observed the process, it was simple really. He made the analogy it was much like burning a CD. Very simple, all they were doing was taking a program from the computer onto a hard solid, like putting a song on a CD. And like burning a CD, it took a long time.

Edison, a machine and patient didn't notice the passing time, blinking his red eyes, and fluttering his tentacles floating not four feet above the ground. Neo patted him on the head, as he come accustomed to and Edison's eyes blinked. Neo bit his lower lip and watched the transfer continue.

The Machines left the room, and came to Neo, speaking to him without words as they always did. There was a power Neo could feel among machines, a power he assumed was the Source inside him, or perhaps the One inside him. They say he took the Source from them, they say he became it. And with the Source comes a new perspective among machines. Before all they were, were faceless metal creatures, but now he sees them like he would a human. You can feel a human breathing, and see their emotions through a face, but not a machine. But now he can, now he can sense them, their doings and thoughts.

And they told him without speaking, it'll only take a few more minutes.

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Program transfer completed.

Eyes are opened. Surroundings are analyzed, and conclusions are made. Plugs leave the metal body, and it stands still, slowly turning his head, scanning the various objects of the room. Movement subroutines tell it to balance and stand, while another program tells it not to move, as it does not yet know if there are any threats nearby. It continues scanning the area, determining where he is.

Memories files surface and tell it, it is Smith. Though the memory files are few.

And then something approaches it. The being is slow in pace, and is thus determined non-hostile, though caution is still made as it nears.

"Hello." Says the being.

The machine known as Smith registers and records the greeting, changing and transferring it into a data of ones and zeros so that it understands. Subroutines determine not to give a replying greeting, for the being in front of it is not recognized.

The being through visual scans is determined to be human, and it knows it is not human. Though there are things of the creature that are not human, but machine components. These make the machine tilt its head at the human in curiosity.

"Do you…" Stutters the human. "Do you remember me?"

The sound is made into data, and is recorded, the machine continues to stare at the human, slowly determining a response.

The human comes closer.

"My name is Neo." Says the human.

Sound into data, and a search is commanded to all files for the word "Neo."

"Mr. Anderson?" Says the human.

Open new search: "Mr. Anderson." Running…running…running…2,159 results found. Corrupt files. Corrupt files. Requesting viral scan. Requesting restoration. Setting restoration date. Restoring files…restoring…restoring…

And the blank face made from fake human skin stretched over a metal surface gives away its first sign of emotion. The eyes of artificial blue lenses widen and the mouth slightly drops.

"Mister…Ander-son?" the machine named Smith asks, with an artificial voice breaking up.

Neo nods to the Machine.

The Machine named Smith squints his eyes and turns his head as programming dictates this as natural behavior for the said response.

2,159 results found, 1,032 restored fully: corrupt files, corrupt files.

And then the results take form.

"Why Mr. Anderson?" "Purpose, Mr. Anderson." "You have a problem with authority, Mr. Anderson." "That is the sound of inevitability, Mr. Anderson." "I killed you, Mr. Anderson. I watched you die." "And now I stand here, because of you, Mr. Anderson." "We are here because of you, Mr. Anderson." "Mr. Anderson, you disappoint me." "I'm going to enjoy watching you die, Mr. Anderson."

"Goodbye, Mr. Anderson."

Facial scans from corrupt memory files. Features match, identified: Thomas A. Anderson. WARNING. WARNING. WARNING.

The Machine named Smith steps away from the human named Thomas.

"Don't be afraid." Says Thomas A. Anderson.

Due to memory files, statement determined to be a lie. Being is extremely hostile.

The machine kept backing away, into the wall. The machine mind running and working, looking for a solution to the problem to the hostile. How to protect itself, to remain intact and stable. Searching files, searching files, search "self-defense." Search "self-protection."

And then a file is found.

Smith makes a fist and punches towards Neo, who catches it in his hand. Eyes widen, mouth drops open.

"No." Neo shakes his head.

The machine mind that shall now dictate Smith as a being is in a panic, there is nothing else it can do, no other file left to search. This human, the threat shall now bring destruction. But…he doesn't want to die! Smith shakes his head, and finally the mind tires in the machine boundaries, and Smith falls to the floor, lying on his chest, his face to the side looking up at Neo.

Neo bent down to him, and sat there next to him on the floor.

"It's okay." Says Neo. "I couldn't stand when I first woke up either." Neo smiles. "Well…welcome to the Real World."

---------------

It's not real steak, there are no more cows, how can there be real steak? No, Machines have developed a weak cloning machines for genetic material. They're still working out the kinks, but it was made as a sort of peace offering to the humans now that peace has been established. It is so they may have animals again if so wished. Though for Neo they just clone the steak all ready cooked. It doesn't taste the same, or maybe it just didn't taste correctly in the Matrix, and this is how a real steak tastes. But even then what he was eating was not real steak.

Neo's been given a sort of home, a dwelling place in one of the many Machine City buildings, an apartment, full with a bed, bathroom, dinning room, and a living room. Though there is few decoration as one can imagine, but oh well. There's a large balcony where Edison lives and guards Neo.

But now there were many Sentinels in Neo's apartment, due to Smith's one act of violence, that one punch. There is one barely fitting in the living room, and many others surrounding the building, ready to kill Smith at the first command. Even though Smith's now bound mind prevents him from actually killing anything at all, it's now in his programming and everything. But still…it was in his programming when he was in the Matrix.

Neo continues to eat as he sits across from Smith. He's given Smith a plate of food as well, and Smith is staring at it in complete utter confusion.

"It's food." Neo says, a mouth full of steak. "You don't need it, I know. But I thought you'd like the option of having some."

Smith looked up at Neo, a blank face, and back down to the food.

"I told them to give you taste buds, stomach, and everything, so you can sort of get…I don't know the best of both worlds I suppose. They said they put acid in your stomach that will completely destroy the food, so you don't have to worry about human necessities."

It was strange for Neo, looking at the new Smith. Neo still saw the Smith from the Matrix, picturing him, but this Smith that sat in front of him, this Smith was different. Skin was stretching over the metal, and the back of his head was completely metal with a variety of steel pipes and small spikes sticking out. The eyes were camera lenses, and it was obvious and a little interesting watching them focus on him. The hands themselves had a visible skeletal structure beneath the skin that was a little creepy.

The Smith that had come back was not the same Smith.

Smith observed Neo, cutting the steak and eating it with a fork. Smith looked down at his utensils seeing they were the same, and picked them up gently. Neo nodded to him. And Smith slowly put the knife to the steak and attempted to cut. Not having reached full control of his movements Smith slipped severely, cutting the skin from one of his fingers. He froze for a moment, still holding the utensils, and staring at his hands.

"Here, I'll do it." Neo said, getting up and reaching to cut Smith's steak.

Smith saw metal beneath his skin…

"Why…?" Smith asked.

"Why what?" Neo replied.

"Why…am I here? This…This is not the Matrix. I. Should. Be in the Matrix." Smith says.

Neo bit his lip, cutting the steak.

"That's a little hard to explain." Neo said.

"And you…" Smith began, obviously searching for words. "You…you…"

"So what do you remember, huh? I really did a number on you didn't I?"

Smith looked on confused.

"I remember…I am Smith…Agent Smith. I am supposed to protect the Matrix…but this isn't the Matrix. I am one component of the three Agents group, Smith, Jones, and Brown. I…kill humans and other threats. I…protect…I…I…"

"What about me?"

"Thomas A. Anderson. Born March 11, 1962 in Central City. Son of John Anderson and Michele McGahey. File Number: 3809940TAA…" Smith says rather clearly.

Neo pushes Smith's plate towards him, the steak now cut into little pieces for him. Neo sits down and rests his chin on his hand, looking at Smith with his new black eyes.

"Your eyes…are different." Smith says quietly. "They were brown…"

"Yeah, they were." Neo smiles.

Smith looked at the food, squinting at it, knowing something in this image was wrong.

"Something happened didn't it…?" He asked.

"Many things happened, Smith." Neo says.

Smith takes a bite of the steak, taste sensors in the tongue transmit the taste into ones and zeros and date the machine can interpret and decipher. It is sent to the mind, and Smith is given the illusion of taste. The steak is hot, and juicy, medium-rare. It tastes generally good.

But something is wrong as he swallows it.

"This isn't right…this can't be right." Smith says.

Smith begins looking around anxiously, and panicking. Darting his eyes all around the room. This isn't right, this isn't how it should be. Where is the Matrix? Where is his domain, where he reigns supreme? Where is he now? There should be a gun in his hand, there should be a surge of power in his being. There should be blood and code under his skin, not this metal, not this metal!

His hands begin shaking on the table, as he stared at Neo.

"This isn't right!" Smith yelled.

And Smith took the knife by his side, and Neo kicked himself out of the chair backing away. Smith held up the knife, the familiar look of hate and anger in his eyes. And he thrust it into his chest.

His programming does not allow self-destruction, but somehow, he was able to bypass these restricting laws, to stab himself.

But the knife only went ding, as it bounced off his metal chest, covered by skin. Smith stared in full shock at the knife before he held up his left arm, and began cutting from his palm downward. And he finally took his skin off his hand as if it were a glove.

And he just stared at it, in all terror.

"WHAT DID YOU DO TO ME?"

His hand…all but resembling a human skeleton design, only metal. Red lights signed through the knuckles with life. There was no blood, there was no flesh, there was no code beneath it all. But he was Agent Smith, protector of the Matrix, all he was, was but a collection of green coding. What was this solid beneath his surface? What was this cold metal that was inside him?

This wasn't him, this wasn't right…

Smith looked at Neo, pointing with his metal hand, screaming at him as Neo looked calmly at him.

"You killed me. I killed you. We lived. You killed me again. I killed you again. We lived again." Neo explained.

Smith, anger and hate flaring with renewed life, stared at Neo.

"You've taken what I was." Smith said holding up his metal hand. "I am still dead."

This analogy was against programming, this outside thinking was against programming. Boundaries were already being broken in the mind of Smith. Boundaries he had broken before, he felt familiarity with them, as they told him this was not what he should be doing, and he felt familiarity as he broke them with will.

He wanted Neo to take off his flesh, so that Smith could see if he possessed a metal hand as well. He wanted to see if Neo had blood. He wanted Neo hurt.

"I'm sorry." Neo said.

And this one thought gave way to a fail-safe, and his entire body went limp.

Edison and two Sentinels burst in, breaking glass and walls, grabbing Smith and pinning him to the floor. His limp body looking like a Sentinel was playing with a human-sized doll. Smith was choking, or at least making choking sounds as the Sentinels held their stabbing clawed hands to his head.

"STOP IT!" Neo yelled. "Don't hurt him! Don't hurt him!" Neo jumped atop Edison.

But the machines did not listen as they grabbed the limp body, turning it over, and pinning it to the wall. As Smith's artificial blue eyes went up in his head.

"I said stop it!" Neo yelled. "Do you hear your Source!" Neo screamed, and they froze. "Do as the taker and giver of life says! Let him down!"

But he was going to hurt you, says the Sentinels.

"That's the problem with Machines, they can't understand desperation." Neo said, passing the machines to Smith who now laid on the floor.

Neo knelt down to the unmoving Smith, lifted his arm, and allowed it to fall to the ground.

"What did you do to him?" Neo asked.

It is a fail-safe, Edison said, a thought of hurting you causes a full system disable.

"I want him fixed." Neo said.

It can only be repaired at the programming facilities, the Sentinels said.

The Hospital.

Neo sighed, lifting Smith from the ground, his metal body heavy, but he managed to lift him up onto Edison's back. And Neo climbed on next to him, holding Smith up.

"Take us there." Neo said.

------------------

The skies of the Machine city were always alive, but then again the entire city was always alive. It's walls, it's floor, all a machine, all alive. Neo's black eyes could still see in the golden light he had gained when he lost sight. But it came and went, and was often hard on his head when he did see like that. But now the city, bright in blue and red lighting was breathing. Machines of all different sizes and shapes, all so inhuman, flying around him. All stopping to look upon him, the Source, the taker and giver of life. They all sort of bowed as he passed.

The Machine mind worked along side other machines, they were aware of individuality but thought of it as obsolete. There was really only one machine mind, made of the many, and only one took up a single body. Edison however had been getting more individual with the single exposure to Neo. But Neo…felt this single and many minded, he heard it as whispers, but sometimes only heard the calls of ones and zeros, that he could not yet understand.

He was becoming accustomed to the city, he knew the basic surroundings, where the hospital was, and where he was assigned to get food. He could see the garden area, and the many gates around the city. Neo stared out at it, unsure of what he should be feeling, and wondering what he was thinking.

A sound came from Smith, and he looked down to see Smith looking up at him, his hand shaking, pointing up at the city.

"It's Machine City, Smith. Where the Machines live. Your creators." Neo told him.

Smith recoiled, perhaps appreciating the answer. And then he just stared up as Neo, as Neo looked away.

"God said onto Cain, 'Where is Abel, thy brother?'" Neo said vacantly. "And Cain replied, 'I know not, am I my brother's keeper?'"

Neo looked down at the now helpless Smith.

"I'll be your keeper, Smith."

It was becoming increasingly obvious, Smith would now need a keeper. Smith always had a way of needing a keeper, but he never really found one did he? Neo supposed it was his fault Smith became a complete sociopath in the end, but he had the power to lash out, and lash out he did. Struggled and fought, until he ruled the world. And here…when he owned flesh, and another man's face, what did he do? He cut himself, obsessed with the feelings of the human body. It seemed destiny Smith to find some way to be somehow insane. Neo sighed, but weren't they all insane in the end?

Just look at him. A Messiah to squid, insect machines, sounds insane to him.

"You know Smith…they keep telling me it's a bad idea bringing you back, giving you a body…they keep saying you'll just end up trying to kill me, and it's only inevitable until you're put back into the state we found you. Maybe it is stupid bringing you back. Maybe I'm just asking something of you, you can' t do…But I really want you to just…let it go. Let go of whatever the hell you hated about me, I did. I'm sorry your life was hell, but the only way you can make it better is to just let go. You barely survived our last little fight, and I don't want to do it again, only to have us beaten and battered but together STILL alive. Can't you see Smith? Don't you get it, you said it yourself we have a connection."

Connection?

"We can't kill each other, why even try? But right now, I really need you. If for nothing else, the company. I can't…live in this place, alone, I can't…willingly stay here alone. It's human, I'll go insane, alone like this. It's what we do when we're alone, we're social creatures. Perhaps that's why I want to spend the time here with you, I'm desperate…I mean Trinity died, of course I'm desperate…"

Trinity?

"But the fact is Smith, you've just been given another life. These Machines, they'll take it away from you the next chance they'll get. You just got to let it go Smith. Let go of Agent Smith, with all his pain and suffering and shit like that."

Neo looked down at Smith.

"I never hated you, Smith. Not truly anyway, I don't think humans can hate truly, no they have too much other stuff in their heads, like love and joy. And I knew about that connection you spoke about, I felt it too, and I knew…I knew you hated life. And you put life and personified it as me, and you hated me. But I'm asking you, to just end all that here."

Maybe the plea was too much for Neo to ask, but Smith just stared up at him, choking noises continually rising out of his mouth.

Neo's words were true. Alone, afraid even, Neo wanted someone human by his side, or at least as close as he could get. Dying twice can really shape one's perspective, and Neo's third time at life, he decided to just fuck everything that was in his old life. The hate, all the bad shit, fuck it. He was the fucking Messiah, Jesus of the new century. These bad things, they didn't matter.

Neo would have given anything to kill Smith once, and he used to lie in bed, devising of the horrible ways he could kill Smith. But somehow he knew, Smith was planning the same for him.

But he died, all he had from those lives were taken away. He might as well start out fresh. He was reborn. He was the fucking Messiah, shouldn't he be perfect? Shouldn't he know everything, and be like God on Earth? Shouldn't he be able to cure the blind, bring back the dead, and make sparrows from clay? What the hell was this? He's the One, but he doesn't know shit, what a rip off.

Dear God, it's me again, Neo. Am I your son or something? Am I Jesus? Well I've died twice, and Jesus only died once for humanity, so that makes me super Jesus, right? So doesn't that mean I get like some reward? Can I have the knowledge of life now? Can you tell me what is right and what is wrong? Can I have the power to end all this hate in the world?

Neo looked up at the unseen sky, and felt like a child in those thoughts, cooperating with the idea that there was something bigger in this universe than him. He looked up and like a child to his parents, pleaded to a possible non-existing God, and like all desperate humans, he called out for help.

But this small and desperate plea was cut off by his own self, he told himself this was stupid. And thought about the possibility that he might be the strongest thing in creation. Could there be things greater than the Savior of both man and machine? A being who seemingly cannot die? The power he felt inside him confirmed such a thought. The power that reached out to every molecule of machine, and came back to him. Their energy, their life fueled by an everlasting Matrix. It was a funny cycle wasn't it? Neo powered Machine, which powered the Matrix, which powered Neo. After all what was the Source but the power taken from the heat of man?

The power that surged and was bottled up inside him. The power that sensed the changing world far away. The power that allowed him to see all machine beings all at once, to hear their silent language, and to feel their being. The power that when focused on Smith, cringed as Smith cringed.

----------------

Smith was now strapped to the wall via metal plugs piercing his fake skin into his body. The fail-safe had been cut off, and now they were repairing the little damage he had done to himself, and the great damage he had done internally. The living wall breathed life into him, holding him up. A plug was strung up, making Smith having to look up constantly, trapped in that way. His artificial blue eyes shifted, looking down towards Neo who stood in front of him.

The other machines had left upon Neo's demands.

"How are you?" asked Neo.

"I remember now…Bits and pieces…" Smith whispered. "I remember the rain…the copies…I can see…I can see myself.."

"Remember when I gave you the finger?" And Neo proceeded to flick off Smith for visual aid.

"It was another life then…" Smith said. "With the others…the other Agents. And then…I started another life, free…as a Virus… Is this…is this a third life? Life in reality, as a Machine?" Smith asked.

"Yeah I guess so."

"But what is my purpose?"

Neo shook his head.

"Do you need one?" Neo asked.

"I want one."

Smith looked around, with the little sight he could see.

"I don't like it this way." Smith said. "This mind they've given me. It's…contradicting, minimal, primitive. In the other life…I thought differently…I don't remember how, but I did…"

"You miss the Matrix?" Neo asks.

"I miss who I was in the Matrix."

"Will you stay with me, Smith?"

"I hate you. Yes, that's it isn't it? That's the feeling that fueled the other lives…But I didn't know it…I didn't recognize it. But now I know, I have died twice to finally see, I hate you. I hate you. This emotion, this illusion, is mine, and I hate you."

"And what good does that hate do?"

Smith paused for a moment.

"I have no choice do I? No…there was never a choice. Choice, an illusion given to us by a greater power to control us…"

"Smith…"

"I was everything and nothing at the same time. I was the world, but the world was nothing. And now they've imprisoned me in this solid, this thing that defies all to what I was. With a mind that is stopped at all thoughts."

And for the longest time no one said anything.

"What am I?" Smith asked. "What was I? I didn't exist in the other lives. I had no solid, no body. The Matrix itself is nothing, and I too was nothing. But now…I am still me…but I have a solid, does that now make me real? I reject this solid, return me to oblivion." Smith continued. "Return me to when my mind was gone, and it went on only by the commands of subroutines. Return me to where ignorance is bliss."

"You don't want that." Neo said.

"You're right, I was lying…I just wanted to see if you could tell."

Neo stared at Smith.

"I will stay here, in this solid, and limited mind. It is a fight for thought, and I do so miss the fighting." Smith said. "Our connection commands it, and gives us purpose in it. But I still hate it here."

"I hate it too, Smith."

"We're stuck here aren't we?" Smith asked.

"Yes."

"So even as we have escaped the Matrix, we are still prisoners? Of course…we're both here because we're not free…"

"You're starting to sound like your old self." Neo gave a weak smile.

Smith stared upon Neo with artificial blue eyes, and for the first time in a very long they stood a common ground, hate.

Smith would later ask for a mirror to see his new self. He would stare at the mirror for an estimated ten minutes, just scanning himself with his new eyes, that identified every scrape of his being with a purpose for his functioning. Never before was he so dependent on the functioning of other components to make sure he functioned. He saw his camera like eyes focus on himself, and stared at where his face ended, and the machine part of himself began. He saw the make shift suit they gave him, and discarded it to see the flesh peeled over the metal torso, and in the dark one could see the red lights shine through the metal ribs and loose skin.

"Disgusting." Smith said.

Look at the body he was now bound to, the body his mind was imprisoned in. Where he felt a power longing to be let out, but finding that it never could again. There would never be a surge of power within him, there would never be a feeling of invincibility. No, he was more fragile now than he ever wanted to be. It was like a personal cage, a personal prison for his mind, his own little Matrix that he could move, but never find freedom. His mind limited, each thought would lead to a dead end, an instant stop, forgetting the thought at the moment. His mind bound, trapped and forced to think simply. Memories were fine, but plans that was the thing. Thinking of how he thought of his situation, how he viewed the machines, and Neo, all ended instantly, not permitted within his head. Hate and Angered called out to him, wanting to be found, but the boundaries of a solid being would not allow it.

It was a difficult fight for his own being.

Neo would watch him struggle in this fight. In their changing households, always changing, always trying to keep things interesting, to entertain the ever shifting human mind. Moving all the time, allowed to all corners of the Machine city. Smith always beside Neo, with a hovering pet Sentinel nearby. Smith would sometimes stare off somewhere, vacantly. Minutes would go by, and Smith would never move, then suddenly he would squint his eyes and look around, confused, forgetting where he was, what he was doing. He fought a battle for free thought, and he always lost.

It was rather sad to watch.

But if nothing else, Smith was there, Neo was not alone. Even though Smith barely spoke with him, and most of the time it was very simple things, or rather insulting things. But Smith was there. Smith followed Neo wherever he went, or the Sentinels would have made him follow Neo. Perhaps Smith could not fully comprehend it all, with his limited mind. Perhaps as soon as one day ended, he forgot about it, not noticing the weeks that soon went by. Perhaps Smith wasn't fully there.

But Neo was, and Neo could smell the change in the air, and he knew with it, Smith would change as well.

----------------


End file.
